Molecular dynamics simulation study of the positioning and dynamics of α-tocopherol in phospholipid bilayers.

Using molecular dynamics simulations, we investigate the interaction of α-tocopherol (α-toc) with dipalmitoylphosphatidylcholine (DPPC), dimyristoylphosphatidylcholine (DMPC), palmitoyloleoylphosphatidylcholine (POPC), and palmitoyloleoylphosphatidylethanolamine (POPE) lipid bilayers. The goal is to develop a better understanding of the positioning and orientation of α-toc inside the bilayers; properties of significant relevance to α-toc anti-oxidant activity. We investigated bilayer systems with 128 lipids in the presence of either single or 14 α-toc molecules. The single α-toc bilayer systems were investigated via biased MD simulations in which the potential of mean force (PMF) and diffusivity were obtained as functions of the distance between α-toc head group and bilayer center. The higher α-toc concentration systems were investigated with unbiased MD simulations. For all four bilayers at both concentrations, the simulations show that the most probable location of the α-toc hydroxyl group is just below the lipid carbonyl group. Overall, the simulation results are in good agreement with existing experimental data except for the DMPC bilayer system for which some experiments predict α-toc to be located closer to bilayer center. The flip-flop frequency calculated shows that the α-toc flip-flop rate is sensitive to bilayer lipid type. In particular, α-toc has a much lower flip-flop rate in a POPE bilayer compared to the three PC lipid bilayers due to the smaller area per lipid in the POPE bilayer. For DMPC and POPC, the α-toc flip-flop rates are significantly higher at higher α-toc concentration and this appears to be related to the local structural disruption caused by α-toc clusters spanning the bilayer.

THE ROLE OF THE ASYMMETRIC BOLAAMPHIPHILIC CHARACTER OF VECAR ON THE KINETIC AND STRUCTURAL ASPECTS OF ITS SELF-ASSEMBLY: A MOLECULAR DYNAMICS SIMULATION STUDY.

VECAR are novel bolaamphiphilic molecules consisting of two hydrophilic molecular groups, a carnosine derivative and a chromanol group, covalently linked by a hydrophobic alkyl spacer of varying length. Despite the potential for application in various biomedical applications VECAR properties, including their bulk properties, are still largely unknown. The early stage of the self-assembly process of VECAR molecules in water is studied using molecular dynamics simulations. The study reveals that the length of the hydrophobic spacer in VECAR affects the aggregation kinetics as well as the size, shape, density, and atomistic structure of the self-assembled aggregates. A mechanism based on cooperative interactions between water, the hydrophilic hydroxyl group, and the hydrophobic benzene ring of the chromanol head is proposed to explain the ordered packings of chromanols in the self-assembled aggregate structures at the aggregate-water interface.

Complexation of Lignin Dimers with ß-Cyclodextrin and Binding Stability Analysis by ESI-MS, Isothermal Titration Calorimetry, and Molecular Dynamics Simulations.

Lignin derived from lignocellulosic biomass is the largest source of renewable bioaromatics present on earth and requires environmentally sustainable separation strategies to selectively obtain high-value degradation products. Applications of supramolecular interactions have the potential to isolate lignin compounds from biomass degradation fractions by the formation of variable inclusion complexes with cyclodextrins (CDs). CDs are commonly used as selective adsorbents for many applications and can capture guest molecules in their internal hydrophobic cavity. The strength of supramolecular interactions between CDs and lignin model compounds that represent potential lignocellulosic biomass degradation products can be characterized by assessing the thermodynamics of binding stability. Consequently, the inclusion interactions of ß-CD and lignin model compounds G-(ß-O-4')-G, G-(ß-O-4')-truncG (guaiacylglycerol-ß-guaiacyl ether), and G-(ß-ß')-G (pinoresinol) were investigated empirically by electrospray ionization mass spectrometry and isothermal titration calorimetry, complemented by molecular dynamics (MD) simulations. Empirical results indicate that there are substantial differences in binding stability dependent on the linkage type. The lignin model ß-ß' dimer showed more potential bound states including 1:1, 2:1, and 1:2 (guest:host) complexation and, based on binding stability determinations, was consistently the most energetically favorable guest. Empirical results are supported by MD simulations that reveal that the capture of G-(ß-ß')-G by ß-CD is promising with a 66% probability of being bound for G-(ß-O-4')-truncG compared to 88% for G-(ß-ß')-G (unbiased distance trajectory and explicit counting of bound states). These outcomes indicate CDs as a promising material to assist in separations of lignin oligomers from heterogeneous mixtures for the development of environmentally sustainable isolations of lignin compounds from biomass fractions.

Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations.

The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ∼45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.

Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics.

Nonequilibrium molecular dynamics (MD) simulations were used to study the effect of three chemical surface groups on the separation of DNA mononucleotide velocity (or time-of-flight) distributions as they pass through nanoslits. We used nanoslits functionalize with self-assembled monolayers (SAMs) since they have relatively smooth surfaces. The SAM molecules were terminated with either a methyl, methylformyl, or phenoxy group, and the nucleotides were driven electrophoretically with an electric field intensity of 0.1 V/nm in slits about 3 nm wide. Although these large driving forces are physically difficult to achieve experimentally, the simulations are still of great value as they provide molecular level insight into nucleotide translocation events and allow comparison of different surfaces. Nucleotides adsorbed and desorbed from the slit surface multiple times during the simulations. The required slit length for 99% accuracy in identifying the deoxynucleotide monophosphates (dNMPs), based on the separation of the distributions of time of flight, was used to compare the surfaces with shorter lengths indicating more efficient separation. The lengths were 6.5 µm for phenoxy-terminated SAMs, 270 µm for methylformyl-terminated SAMs, and 2400 µm for methyl-terminated SAMs. Our study showed that a slit with a section with methyl termination and the second section with methylformyl termination lead to a required length of 120 µm, which was significantly lower than for only a methylformyl- or methyl-terminated surface.

Interaction of lignin dimers with model cell membranes: A quartz crystal microbalance and molecular dynamics simulation study.

A study of the interaction between cell membranes and small molecules derived from lignin, a protective phenolic biopolymer found in vascular plants, is crucial for identifying their potential as pharmacological and toxicological agents. In this work, the interactions of model cell membranes [supported 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayers] are compared for three ßO4 dimers of coniferyl alcohol (G lignin monomer): guaiacylglycerol guaiacol ester with a hydroxypropenyl (HOC3H4-) tail (G-ßO4'-G), a truncated GG dimer without HOC3H4- (G-ßO4'-truncG), and a benzylated GG dimer (benzG-ßO4'-G). The uptake of the lignin dimers (per mass of lipid) and the energy dissipation (a measure of bilayer disorder) are higher for benzG-ßO4'-G and G-ßO4'-truncG than those for G-ßO4'-G in the gel-phase DPPC bilayer, as measured using quartz crystal microbalance with dissipation (QCM-D). A similar uptake of G-ßO4'-truncG is observed for a fluid-phase bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine, suggesting that the effect of the bilayer phase on dimer uptake is minimal. The effects of increasing lignin dimer concentration are examined through an analysis of density profiles, potential of mean force curves, lipid order parameters, and bilayer area compressibilities (disorder) in the lipid bilayers obtained from molecular dynamics simulations. Dimer distributions and potentials of mean force indicate that the penetration into bilayers is higher for benzG-ßO4'-G and G-ßO4'-truncG than that for G-ßO4'-G, consistent with the QCM-D results. Increased lipid tail disorder due to dimer penetration leads to a thinning and softening of the bilayers. Minor differences in the structure of lignin derivatives (such as truncating the hydroxypropenyl tail) have significant impacts on their ability to penetrate lipid bilayers.

Umbrella sampling simulations of biotin carboxylase: is a structure with an open ATP grasp domain stable in solution?

Biotin carboxylase is a homodimer that utilizes ATP to carboxylate biotin. Studies of the enzyme using X-ray crystallography revealed a prominent conformational change upon binding ATP. To determine the importance of this closing motion, the potential of mean force with the closure angle as a reaction coordinate was calculated using molecular dynamics simulations and umbrella sampling for a monomer of Escherichia coli biotin carboxylase in water with restraints to simulate attachment to a surface. The result suggests that the most stable state for the enzyme is a closed state different from both the ATP-bound and open state X-ray crystallography structures. There is also a significant motion of a region near the dimer interface not predicted by considering only open and closed configurations, which may have implications for the dynamics and activity of the dimer.

Experimental and Molecular Dynamics Simulation Study of the Effects of Lignin Dimers on the Gel-to-Fluid Phase Transition in DPPC Bilayers.

High resolution differential scanning calorimetry (DSC) and molecular dynamics (MD) simulations were used to investigate the effect of three lignin dimers on the gel to fluid phase transition in DPPC lipid bilayers. The goal of this research is to begin to understand the partitioning of model lignin dimers into lipid bilayers and its effects on the gel to fluid transition temperature (Tm). The long-term objective is to establish structure-function relationships for well-defined lignin derivatives at biologically relevant surfaces. This work uses a newly synthesized guiacylglycerol guaiacol ester with a hydroxypropenyl (HOC3H4-) group resembling natural lignin (GG dimer), compared with a truncated GG dimer without the HOC3H4- and benzyl-modified GG dimers. The DSC results show that the dimer most like natural lignin (with a hydroxypropenyl tail) has log K = 2.72 ± 0.05, and MD simulations show that it associates with the headgroups of the lipid but does not penetrate strongly into the interior of the bilayer. Therefore, this dimer has little effect on the Tm value. In contrast, the truncated dimer, which has been used as a representative GG dimer in prior studies, partitions into the bilayer, as seen in MD simulations, and shifts Tm because of its increased lipophilicity (DSC log K = 3.45 ± 0.20). Similarly, modification of the natural GG dimer by benzylation of the phenol makes it lipophilic (DSC log K = 3.38 ± 0.28), causing it to partition into the bilayer, as seen in MD simulations and shift Tm. In MD, we capture the transition from gel to fluid phase by defining and analyzing a normalized deuterium order parameter averaged over all carbon atoms located in the middle of the lipid tails. In this way, the phase transition can be clearly observed and, importantly, MD results show the same trend of transition temperature shifts as the DSC results. Furthermore, we compare partition coefficients estimated from free energy profiles calculated in MD to those obtained from experiment and they are in qualitative agreement. The success at predicting the structural effects of lignin dimers on lipid bilayers suggests that MD simulations can be used in the future to screen the interactions of lignin oligomers and their derivatives with lipid bilayers.

Interfacial states and far-from-equilibrium transitions in the epitaxial growth and erosion on (110) crystal surfaces.

We discuss the far-from-equilibrium interfacial phenomena occurring in the multilayer homoepitaxial growth and erosion on (110) crystal surfaces. Experimentally, these rectangular symmetry surfaces exhibit a multitude of interesting nonequilibrium interfacial structures, such as the rippled one-dimensional periodic states that are not present in the homoepitaxial growth and erosion on the high symmetry (100) and (111) crystal surfaces. Within a unified phenomenological model, we reveal and elucidate this multitude of states on (110) surfaces as well as the transitions between them. By analytic arguments and numerical simulations, we address experimentally observed transitions between two types of rippled states on (110) surfaces. We discuss several intermediary interface states intervening, via consecutive transitions, between the two rippled states. One of them is the rhomboidal pyramid state, theoretically predicted by Golubovic [Phys. Rev. Lett. 89, 266104 (2002)] and subsequently seen, by de Mongeot and co-workers, in the epitaxial erosion of Cu(110) and Rh(110) surfaces [A. Molle, Phys. Rev. Lett. 93, 256103 (2004), and A. Molle, Phys. Rev. B 73, 155418 (2006)]. In addition, we find a number of interesting intermediary states having structural properties somewhere between those of rippled and pyramidal states. Prominent among them are the rectangular rippled states of long rooflike objects (huts) recently seen on Ag(110) surface. We also predict the existence of a striking interfacial structure that carries nonzero, persistent surface currents. Periodic surface currents vortex lattice formed in this so-called buckled rippled interface state is a far-from-equilibrium relative of the self-organized convective flow patterns in hydrodynamic systems. We discuss the coarsening growth of the multitude of the interfacial states on (110) crystal surfaces.

Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study.

There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide-wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide-wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide-wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.

Distinguishing single DNA nucleotides based on their times of flight through nanoslits: a molecular dynamics simulation study.

Transport of single molecules in nanochannels or nanoslits might be used to identify them via their transit (flight) times. In this paper, we present molecular dynamics simulations of transport of single deoxynucleotide 5'-monophoshates (dNMP) in aqueous solution under pressure-driven flow, to average velocities between 0.4 and 1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulation results show that, while moving along the slit, the mononucleotides are adsorbed and desorbed from the walls multiple times. For the simulations, the estimated minimum slit length required for separation of the dNMP flight time distributions is about 5.9 µm, and the minimum analysis time per dNMP is about 10 µs. These are determined by the nature of the nucleotide-wall interactions, channel width, and by the flow characteristics. A simple analysis using realistic dNMP velocities shows that, in order to reduce the effects of diffusional broadening and keep the analysis time per dNMP reasonably small, the nucleotide velocity should be relatively high. Tailored surface chemistry could lead to further reduction of the analysis time toward its minimum value for a given driving force.

Molecular dynamics simulation study of the effect of DMSO on structural and permeation properties of DMPC lipid bilayers.

We present molecular dynamics simulations of dimyristoylphosphatidylcholine (DMPC) lipid bilayers in the presence of dimethyl sulfoxide (DMSO). The MD simulations focus on understanding the effect of 3 mol % DMSO on structural and permeation properties of DMPC bilayers. The potential of mean force (PMF) and the diffusivity profiles along the normal direction to the bilayer were calculated for water and DMSO molecules in systems containing 0 and 3 mol % DMSO. The simulation results indicate that while the presence of DMSO has only a small effect on diffusion coefficients of both water and DMSO molecules, it affects significantly the corresponding trans-membrane free energy profiles. Using the free energy profiles and diffusivities for water and DMSO and by employing an inhomogeneous solubility-diffusion model we calculated the permeability coefficients. Our simulations show that the increase of the concentration of DMSO in the solution to 3 mol % leads to a significant increase, by about 3 times, of the permeability of water through a DMPC bilayer; a permeability increase that might explain in part the unusual ability of DMSO, even at relatively low concentrations, to reduce the osmotic pressure imbalance present during cryopreservation protocols.

Epitaxial growth and erosion on (110) crystal surfaces: structure and dynamics of interfacial States.

We study nonequilibrium interfacial states in multilayer epitaxial growth and erosion on rectangular symmetry crystal surfaces. We elucidate a recently observed transition between two kinds of rippled states on (110) surfaces. We predict several novel interface states intervening, via consecutive transitions, between the two rippled states. We predict coarsening laws of the dynamics of the rippled and the intervening states on (110) crystal surfaces.

Scaling behavior of grain-rotation-induced grain growth.

Recent investigations of grain growth in nanocrystalline materials have revealed a new growth mechanism: grain-rotation-induced grain coalescence. Based on a simple model employing a stochastic theory and using computer simulations, here we investigate the coarsening of a polycrystalline microstructure due solely to the grain-rotation coalescence mechanism. Our study demonstrates that this mechanism exhibits power-law growth with a universal scaling exponent. The value of this universal growth exponent is shown to depend on the assumed mechanism by which the grain rotations are accommodated.